[gmx-users] how to know solvent molecule number

Justin Lemkul jalemkul at vt.edu
Wed Apr 5 15:43:10 CEST 2017

On 4/5/17 9:12 AM, Chintan Bhagat wrote:
> Hello,
> I want to do stimulation of my protein in solvent, ethanolamine (different
> percentage).
> I have made box of 1 nm and then using command
> "gmx solvate -cp 1AKI_newbox.gro -cs ethanolamine.gro -o 1AKI_solv.gro -p
> topol.top",
> As per my knowledge, i solvated my protein in ethanolamine.
> Now I want to know the number of ethanolamine molecule present in box. Then
> I looked in to *.top* file but no information is availble in the file (SOL).
> (As per intruction, program is only hard-coded to update the topology in
> the case of water).
> I found increase in number of molecules from 7200 to 128004 in
> /home/lab1/Desktop/md2/1AKI_processed.gro.gro and 1AKI_solv.gro,
> respectively. It means something is inserted in box (must be
> ethanolamine!!!!!-my guess)
> How can i know number of ethanolamine molecules?

Use grep -c with a unique atom name to count the number of any given molecule in 
the system.

> for reference please find attched files.

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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